read_Ct_wide {RQdeltaCT}

read_Ct_wide

Description

This function imports Ct data in a wide-format table with sample names given in columns.

Usage

read_Ct_wide(path.Ct.file, path.design.file, sep, dec)

Arguments

path.Ct.file

Path to wide-format table in .txt or csv. format with Ct values. This table must contain gene names in the first column, and sample names in the first row (genes by rows and samples by columns).

path.design.file

Path to table in .txt or csv. file that contains two columns: column named "Sample" with names of samples and column named "Group" with names of groups assigned to samples. The names of samples in this file must correspond to the names of columns in the file with Ct values.

sep

Character of a field separator in both imported files.

dec

Character used for decimal points in Ct values.

Details

This function needs two files to import: a wide-format table with Ct values and an additional file with group names (see parameters path.Ct.file and path.design.file for further details on tables structure). Both files are merged to return a long-format table ready for analysis. All parameters must be specified; there are no default values.

Value

Data frame in long format ready to analysis.

Examples

path.Ct.file <- system.file("extdata",
                            "data_Ct_wide.txt",
                            package = "RQdeltaCT")
path.design.file <- system.file("extdata",
                                "data_design.txt",
                                package = "RQdeltaCT")

library(tidyverse)
data.Ct <- read_Ct_wide(path.Ct.file = path.Ct.file,
                        path.design.file = path.design.file,
                        sep ="\t",
                        dec = ".")
str(data.Ct)